WASHINGTON — President Barack Obama has threatened to veto the 2014 National Defense Authorization Act if it includes a section requiring protection of the religious beliefs of military personnel.

On June 5, the House Armed Services Committee adopted an amendment to H.R. 1960, the defense appropriations bill. It specified that "the armed forces shall accommodate the beliefs, actions and speech" that reflect the "conscience, moral principles or religious beliefs" of its members, except in cases of military necessity.

On June 11, the White House released a "Statement of Administration Policy" (SAP) on the bill, which stated that the administration "strongly objects to Section 530" on the grounds that "this provision would have a significant adverse effect on good order, discipline, morale and mission accomplishment."

The SAP specified numerous other areas of White House disagreement with H.R. 1960 and warned that, if passed in its present form, "the president’s senior advisers would recommend that the president veto the bill."

Ambassador Ken Blackwell, former U.S. ambassador to the United Nations Human Rights Commission, denounced the implied threat to veto the appropriations bill because of its inclusion of religious conscience protections.

"President Obama is waging a war on religion," Blackwell told Breitbart News. "He and [Secretary of Defense] Chuck Hagel are denying the most basic rights to those who put their lives on the line to protect all of our rights. It is shameful and appalling. I am confident that congressional leadership will show courage to stand up for our troops against this radical assault on religious liberty in the military."

The president’s opposition to the religious-freedom provision in the bill is the latest in a rash of incidents over the last few years that have left Catholic and other Christian leaders concerned about threats to the religious freedom of Christians in the ranks.

"There have been an increasing number of events that, when taken together, demonstrate a pattern of hostility towards religious freedom in the military," Rep. Randy Forbes, R-Va., a member of the House Armed Services Committee, told the Register.

For Catholic and Christian leaders, sensational reports of the U.S. military perpetrating religious-freedom violations, and unfounded allegations that President Obama is behind them, have served to obscure more concrete concerns about the freedom of Christians in the military.

These concerns intensified following the September 2011 repeal of the military’s "Don’t Ask, Don’t Tell" (DADT) policy, thereby allowing open homosexuals to join the military, and the Obama administration’s policies extending protections to same-sex couples. And Christians in the military are monitoring the U.S. Supreme Court ruling on the constitutionality of the Defense of Marriage Act, the federal law that defines marriage as the union of a man and a woman, as a decision overturning DOMA could dramatically impact the religious freedom of chaplains and soldiers.

The Southern Baptist Convention (SBC) released a statement in May to alert Christians to inaccurate reports, such as the one that alleged the Air Force had hired Mikey Weinstein of the Military Religious Freedom Foundation (known for making inflammatory statements about Christians) as a consultant. Weinstein had only requested and was granted a meeting with officials. The SBC also stated it was not true that its website had been blocked on Army bases "for ideological reasons," but, instead, was an issue reported on multiple military bases, not just Army ones, caused by malware.

"These reports have elicited a great deal of concern and confusion among military chaplains, pastors and congregations," the Southern Baptist Convention stated, adding that some cases where fact mixed with fiction were potentially "furthering already tense relationships between military and religious communities."


Troublesome Incidents

However, some credible reports have involved military officials severing associations with Christianity as part of a policy of avoiding any appearance of religious favoritism: removal of crosses from an Army base in Afghanistan or the Air Force Academy discontinuing its sponsorship of Operation Christmas Child (due to its ties to evangelicals). Both cases were prompted by complaints from the group American Atheists and Weinstein’s foundation, respectively.

More recently, an Army instructor crafted a presentation for Army Reserve officers in Pennsylvania that lumped in Catholics and evangelical Christians with extremists like al Qaeda. After an outcry, the U.S. Army investigated, and it said that the materials were corrected, and the instructor apologized.

Forbes said that the influence of the DoD civilian leadership and outside groups, not military commanders, was behind many of these incidents. But taken together they were creating the impression of a more hostile climate for religious freedom in the armed forces.

"If gone unchecked, over time, it will result in a more uniformly accepted attitude that religious freedom is neither important nor protected," he said.


Proselytizing vs. Evangelizing

Media reports that the Department of Defense had banned religious proselytizing, possibly punishable by court martial or non-judicial punishments, set off a firestorm.

The Pentagon later clarified that it did not mean to equate proselytizing with sharing one’s faith or "evangelizing," but was referring to coercing or harassing another person to change his or her religion.

"In general, service members may share their faith with other service members, but may not forcibly attempt to convert others of any faith or no faith to their own beliefs," Lt. Cmdr. Nate Christensen, a Department of Defense spokesman, told the Register.

The Southern Baptist Convention cited this incident in its May statement as a concern. While it condemned coercion to faith in Christ, it emphasized the Pentagon’s "seemingly arbitrary distinction" between evangelism and proselytizing could leave one service member thinking he was engaging in "a friendly conversation about spiritual matters" that another could either perceive or characterize as proselytizing. It predicted that there could be "a chilling effect on service personnel sharing their faith at all."

However, Christensen told the Register that concerns about these issues are "handled on a case-by-case basis."

He did confirm that the Department of Defense does not have a policy addressing religious proselytizing, nor has there been any attempt to change the Uniform Code of Military Justice "to make religious proselytizing a specific offense."

Forbes, however, said he was "concerned by any measurement for disciplinary action that was not properly defined by law or policy."


Other Concerns

Joseph La Rue, an attorney with the public advocacy firm Alliance Defending Freedom (ADF), told the Register that ADF is investigating the extent of violations of Christian religious liberty and how far up the chain of command they go.

"I think there is definitely a reason to be concerned," he said. "Are we dealing with isolated incidents that were mistakes or are we dealing with something bigger than that? Right now, frankly, we don’t know."

However, he said a number of incidents involve Christians who have articulated their views on homosexuality. ADF is a consultant on one such case involving the reprimanding of a U.S. Army master sergeant who bought Chick-fil-A — the fast-food chain targeted by homosexual-rights supporters after its president expressed support for traditional marriage — to celebrate his promotion and vocalize his support for DOMA.

"There’s a tension between religious freedom on the one hand and full acceptance of homosexual members of the military on the other hand," La Rue said.

Archbishop Timothy Broglio, head of the U.S. Archdiocese for the Military Services, told the Register that some incidents involving Christians are taken out of context and get "overreported," resulting in overreactions. But he said the situation for Catholics in the military is "one that is in transition," especially now that DADT is gone.

"We as Catholics have a very fine line to walk between respect for people with other sexual preferences and being very clear on what the doctrine of the Church is, as taught in the Catechism of the Catholic Church."

Archbishop Broglio told the Register that chaplains have solid First Amendment protections "in purely catechetical and religious settings."

"The question is when we leave those settings — a counseling situation, for example — the area becomes more murky and the distinctions a little less clear," he said, pointing out that a chaplain has both his spiritual duties and the duties of an officer to perform.

"If a homosexual couple comes for counseling, a Catholic chaplain would have to find someone else to give them that counseling."

He said the situation probably would become even more complicated if the Supreme Court chooses to strike down DOMA. A Catholic chaplain tasked with organizing the "Strong Bonds" retreat for Army families, for example, may find himself in the position of having to bow out if it requires him to treat same-sex couples as equivalent to married couples.

"But for now that is not permitted, because DOMA is the law of the land," Archbishop Broglio said.

Forbes said that Congress previously had included legislation in the National Defense Authorization Act (NDAA) 2013 designed to protect the religious and conscience rights of Christians in the wake of the passage of DADT.

But he was gravely concerned that the Department of Defense still had not implemented those guidelines, which state, "The armed forces shall accommodate the beliefs of a member of the armed forces reflecting the conscience, moral principles or religious beliefs of the member and, in so far as practicable, may not use such beliefs as the basis of any adverse personnel action, discrimination or denial of promotion, schooling, training or assignment."

In signing the 2013 bill into law, Obama stated the conscience clause, known as Sec. 533, was "unnecessary and ill-advised."

"The military already appropriately protects the freedom of conscience of chaplains and service members," he said in the bill’s signing statement.

La Rue said that the ADF is not satisfied with the Department of Defense’s handling of alleged violations of Christians’ religious liberty because incidents continue to happen.

He said ADF is also involved in cases that center on chaplains allegedly disciplined for invoking the Bible in chaplaincy programs.

"These incidents, whether they are isolated or intentional, have a tendency to make Christians think twice about the military," he said.

Forbes said that he is concerned over these incidents cultivating "a culture of silence," which he called a "subtle but significant threat to religious freedom in the military."

Said the Virginia congressman, "It is dangerous to cultivate an environment that implicitly or explicitly communicates to people of faith that they have the freedom to believe what they wish, but that those beliefs should not be reflected in the way they live their personal and professional lives."


Peter Jesserer Smith writes from Rochester, New York.

Register staff contributed

to this report.